{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Juvenile\" and experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\"", "rows": [[25326, "SRR25868015", "SRX21589423", "SRS18766996", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "vaccinated+SVCV  scRNAseq Kidney leukocyte", "GSM7749529", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV|geo loc name:missing|collection date:missing", "vaccinated+SVCV  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV", "GSM7749529", "GSM7749529: vaccinated+SVCV  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749529 r1", "GSM7749529", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz", "fastq fastq", 48964415682.0, 411465678.0, "GSM7749529 r1", "0:28 1:91", "A:13575624351;C:10984755198;G:11582424564;T:12820058148;N:1553421", 28, 91, null, null, 13575624351, 10984755198, 11582424564, 12820058148, 1553421, "SRX21589423", "SRS18766996", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00754, 0.93029, 0.00274, 0.13414, 0.99168, 0.81527, 0.35, 0.50044, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [25327, "SRR25868016", "SRX21589422", "SRS18766995", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "SVCV  scRNAseq Kidney leukocyte", "GSM7749528", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV|geo loc name:missing|collection date:missing", "SVCV  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV", "GSM7749528", "GSM7749528: SVCV  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749528 r1", "GSM7749528", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "SVCV_S1_L001_R2_001.fastq.gz SVCV_S1_L001_R1_001.fastq.gz", "fastq fastq", 48037908933.0, 403679907.0, "GSM7749528 r1", "0:28 1:91", "A:13476452185;C:10712519121;G:11200837365;T:12646404590;N:1695672", 28, 91, null, null, 13476452185, 10712519121, 11200837365, 12646404590, 1695672, "SRX21589422", "SRS18766995", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00795, 0.92383, 0.00261, 0.14, 0.98948, 0.7806, 0.36862, 0.54549, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [25328, "SRR25868017", "SRX21589421", "SRS18766994", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "PBS  scRNAseq Kidney leukocyte", "GSM7749527", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS|geo loc name:missing|collection date:missing", "PBS  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS", "GSM7749527", "GSM7749527: PBS  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749527 r1", "GSM7749527", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz", "fastq fastq", 49559940115.0, 416470085.0, "GSM7749527 r1", "0:28 1:91", "A:13856071803;C:11114011608;G:11616674427;T:12971434952;N:1747325", 28, 91, null, null, 13856071803, 11114011608, 11616674427, 12971434952, 1747325, "SRX21589421", "SRS18766994", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00648, 0.92681, 0.00213, 0.1376, 0.99056, 0.79866, 0.40117, 0.5487, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [26558, "SRR26173859", "SRX21885960", "SRS18977085", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 F17 R1", "GSM7804200", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 F17 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804200", "GSM7804200: V2a sample2 354 F17 R1; Danio rerio; RNA Seq", "GSM7804200 r1", "GSM7804200", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_F17_R1.fastq.gz", "fastq", 26979490.0, 627430.0, "GSM7804200 r1", "0:43", "A:7493119;C:5872644;G:6013311;T:7600416;N:0", 43, null, null, null, 7493119, 5872644, 6013311, 7600416, 0, "SRX21885960", "SRS18977085", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.82979, null, 0.33034, null, 0.94253, null, 0.53995, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26559, "SRR26173860", "SRX21885959", "SRS18977083", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 F16 R1", "GSM7804199", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 F16 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804199", "GSM7804199: V2a sample2 354 F16 R1; Danio rerio; RNA Seq", "GSM7804199 r1", "GSM7804199", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_F16_R1.fastq.gz", "fastq", 26312130.0, 611910.0, "GSM7804199 r1", "0:43", "A:7117249;C:5957278;G:6103577;T:7134026;N:0", 43, null, null, null, 7117249, 5957278, 6103577, 7134026, 0, "SRX21885959", "SRS18977083", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87071, null, 0.23579, null, 0.90678, null, 0.52226, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26560, "SRR26173861", "SRX21885958", "SRS18977084", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 F15 R1", "GSM7804198", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 F15 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804198", "GSM7804198: V2a sample2 354 F15 R1; Danio rerio; RNA Seq", "GSM7804198 r1", "GSM7804198", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_F15_R1.fastq.gz", "fastq", 32073872.0, 745904.0, "GSM7804198 r1", "0:43", "A:8695962;C:7255833;G:7422516;T:8699561;N:0", 43, null, null, null, 8695962, 7255833, 7422516, 8699561, 0, "SRX21885958", "SRS18977084", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86262, null, 0.24391, null, 0.90881, null, 0.52511, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26561, "SRR26173862", "SRX21885957", "SRS18977081", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 F14 R1", "GSM7804197", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 F14 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804197", "GSM7804197: V2a sample2 354 F14 R1; Danio rerio; RNA Seq", "GSM7804197 r1", "GSM7804197", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_F14_R1.fastq.gz", "fastq", 31158875.0, 724625.0, "GSM7804197 r1", "0:43", "A:8769852;C:6707813;G:6866255;T:8814955;N:0", 43, null, null, null, 8769852, 6707813, 6866255, 8814955, 0, "SRX21885957", "SRS18977081", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.8739, null, 0.27254, null, 0.9246, null, 0.54185, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26562, "SRR26173863", "SRX21885956", "SRS18977082", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 F13 R1", "GSM7804196", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 F13 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804196", "GSM7804196: V2a sample2 354 F13 R1; Danio rerio; RNA Seq", "GSM7804196 r1", "GSM7804196", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_F13_R1.fastq.gz", "fastq", 41289804.0, 960228.0, "GSM7804196 r1", "0:43", "A:11114918;C:9358398;G:9568761;T:11247727;N:0", 43, null, null, null, 11114918, 9358398, 9568761, 11247727, 0, "SRX21885956", "SRS18977082", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.82861, null, 0.29409, null, 0.93235, null, 0.49485, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26563, "SRR26173864", "SRX21885955", "SRS18977079", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 F12 R1", "GSM7804195", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 F12 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804195", "GSM7804195: V2a sample2 354 F12 R1; Danio rerio; RNA Seq", "GSM7804195 r1", "GSM7804195", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_F12_R1.fastq.gz", "fastq", 30569259.0, 710913.0, "GSM7804195 r1", "0:43", "A:8286806;C:6854804;G:7028453;T:8399196;N:0", 43, null, null, null, 8286806, 6854804, 7028453, 8399196, 0, "SRX21885955", "SRS18977079", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.80426, null, 0.29136, null, 0.94123, null, 0.54305, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26564, "SRR26173865", "SRX21885954", "SRS18977080", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 F11 R1", "GSM7804194", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 F11 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804194", "GSM7804194: V2a sample2 354 F11 R1; Danio rerio; RNA Seq", "GSM7804194 r1", "GSM7804194", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_F11_R1.fastq.gz", "fastq", 29626097.0, 688979.0, "GSM7804194 r1", "0:43", "A:8063765;C:6645347;G:6803778;T:8113207;N:0", 43, null, null, null, 8063765, 6645347, 6803778, 8113207, 0, "SRX21885954", "SRS18977080", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.84972, null, 0.26423, null, 0.9234, null, 0.54087, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26565, "SRR26173866", "SRX21885953", "SRS18977078", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 F10 R1", "GSM7804193", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 F10 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804193", "GSM7804193: V2a sample2 354 F10 R1; Danio rerio; RNA Seq", "GSM7804193 r1", "GSM7804193", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_F10_R1.fastq.gz", "fastq", 24594409.0, 571963.0, "GSM7804193 r1", "0:43", "A:6605642;C:5535165;G:5682586;T:6771016;N:0", 43, null, null, null, 6605642, 5535165, 5682586, 6771016, 0, "SRX21885953", "SRS18977078", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.77683, null, 0.28872, null, 0.94633, null, 0.52513, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26566, "SRR26173867", "SRX21885952", "SRS18977077", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 E9 R1", "GSM7804168", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 E9 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804168", "GSM7804168: V2a sample2 354 E9 R1; Danio rerio; RNA Seq", "GSM7804168 r1", "GSM7804168", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_E9_R1.fastq.gz", "fastq", 33259941.0, 773487.0, "GSM7804168 r1", "0:43", "A:9004615;C:7506729;G:7674909;T:9073688;N:0", 43, null, null, null, 9004615, 7506729, 7674909, 9073688, 0, "SRX21885952", "SRS18977077", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85528, null, 0.32094, null, 0.89217, null, 0.50224, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26567, "SRR26173868", "SRX21885951", "SRS18977076", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 E8 R1", "GSM7804167", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 E8 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804167", "GSM7804167: V2a sample2 354 E8 R1; Danio rerio; RNA Seq", "GSM7804167 r1", "GSM7804167", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_E8_R1.fastq.gz", "fastq", 45348316.0, 1054612.0, "GSM7804167 r1", "0:43", "A:12143243;C:10459395;G:10612458;T:12133220;N:0", 43, null, null, null, 12143243, 10459395, 10612458, 12133220, 0, "SRX21885951", "SRS18977076", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.8783, null, 0.19318, null, 0.88572, null, 0.49101, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26568, "SRR26173869", "SRX21885950", "SRS18977075", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 E7 R1", "GSM7804166", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 E7 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804166", "GSM7804166: V2a sample2 354 E7 R1; Danio rerio; RNA Seq", "GSM7804166 r1", "GSM7804166", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_E7_R1.fastq.gz", "fastq", 30522002.0, 709814.0, "GSM7804166 r1", "0:43", "A:8167984;C:7033955;G:7127866;T:8192197;N:0", 43, null, null, null, 8167984, 7033955, 7127866, 8192197, 0, "SRX21885950", "SRS18977075", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87804, null, 0.20762, null, 0.88418, null, 0.51381, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26569, "SRR26173870", "SRX21885949", "SRS18977074", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 E6 R1", "GSM7804165", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 E6 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804165", "GSM7804165: V2a sample2 354 E6 R1; Danio rerio; RNA Seq", "GSM7804165 r1", "GSM7804165", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_E6_R1.fastq.gz", "fastq", 39095858.0, 909206.0, "GSM7804165 r1", "0:43", "A:10597068;C:8804712;G:8974908;T:10719170;N:0", 43, null, null, null, 10597068, 8804712, 8974908, 10719170, 0, "SRX21885949", "SRS18977074", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.8093, null, 0.38297, null, 0.91545, null, 0.56195, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26570, "SRR26173871", "SRX21885948", "SRS18977073", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 E5 R1", "GSM7804164", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 E5 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804164", "GSM7804164: V2a sample2 354 E5 R1; Danio rerio; RNA Seq", "GSM7804164 r1", "GSM7804164", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_E5_R1.fastq.gz", "fastq", 33632880.0, 782160.0, "GSM7804164 r1", "0:43", "A:9099447;C:7602241;G:7747634;T:9183558;N:0", 43, null, null, null, 9099447, 7602241, 7747634, 9183558, 0, "SRX21885948", "SRS18977073", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.83226, null, 0.28405, null, 0.90715, null, 0.52148, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26571, "SRR26173872", "SRX21885947", "SRS18977072", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 E4 R1", "GSM7804163", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 E4 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804163", "GSM7804163: V2a sample2 354 E4 R1; Danio rerio; RNA Seq", "GSM7804163 r1", "GSM7804163", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_E4_R1.fastq.gz", "fastq", 10823057.0, 251699.0, "GSM7804163 r1", "0:43", "A:3014035;C:2419189;G:2487845;T:2901988;N:0", 43, null, null, null, 3014035, 2419189, 2487845, 2901988, 0, "SRX21885947", "SRS18977072", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85783, null, 0.26946, null, 0.91033, null, 0.52459, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26572, "SRR26173873", "SRX21885946", "SRS18977068", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 E3 R1", "GSM7804162", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 E3 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804162", "GSM7804162: V2a sample2 354 E3 R1; Danio rerio; RNA Seq", "GSM7804162 r1", "GSM7804162", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_E3_R1.fastq.gz", "fastq", 49775381.0, 1157567.0, "GSM7804162 r1", "0:43", "A:13325978;C:11313973;G:11568082;T:13567348;N:0", 43, null, null, null, 13325978, 11313973, 11568082, 13567348, 0, "SRX21885946", "SRS18977068", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.80873, null, 0.29504, null, 0.93791, null, 0.52789, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26573, "SRR26173874", "SRX21885945", "SRS18977070", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 E2 R1", "GSM7804161", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 E2 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804161", "GSM7804161: V2a sample2 354 E2 R1; Danio rerio; RNA Seq", "GSM7804161 r1", "GSM7804161", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_E2_R1.fastq.gz", "fastq", 44072334.0, 1024938.0, "GSM7804161 r1", "0:43", "A:11780930;C:10068667;G:10185567;T:12037170;N:0", 43, null, null, null, 11780930, 10068667, 10185567, 12037170, 0, "SRX21885945", "SRS18977070", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.78009, null, 0.2621, null, 0.943, null, 0.54719, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26574, "SRR26173875", "SRX21885944", "SRS18977071", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 D1 R1", "GSM7804136", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 D1 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804136", "GSM7804136: V2a sample2 354 D1 R1; Danio rerio; RNA Seq", "GSM7804136 r1", "GSM7804136", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_D1_R1.fastq.gz", "fastq", 49923.0, 1161.0, "GSM7804136 r1", "0:43", "A:12799;C:11604;G:11134;T:14386;N:0", 43, null, null, null, 12799, 11604, 11134, 14386, 0, "SRX21885944", "SRS18977071", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.5773, null, 0.18478, null, 0.99472, null, 0.51097, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26575, "SRR26173876", "SRX21885943", "SRS18977069", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 C24 R1", "GSM7804135", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 C24 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804135", "GSM7804135: V2a sample2 354 C24 R1; Danio rerio; RNA Seq", "GSM7804135 r1", "GSM7804135", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_C24_R1.fastq.gz", "fastq", 30735540.0, 714780.0, "GSM7804135 r1", "0:43", "A:7999390;C:7036767;G:7190113;T:8509270;N:0", 43, null, null, null, 7999390, 7036767, 7190113, 8509270, 0, "SRX21885943", "SRS18977069", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.48457, null, 0.16974, null, 0.99328, null, 0.82979, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26576, "SRR26173877", "SRX21885942", "SRS18977067", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 C23 R1", "GSM7804134", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 C23 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804134", "GSM7804134: V2a sample2 354 C23 R1; Danio rerio; RNA Seq", "GSM7804134 r1", "GSM7804134", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_C23_R1.fastq.gz", "fastq", 24386031.0, 567117.0, "GSM7804134 r1", "0:43", "A:6620599;C:5230020;G:5371347;T:7164065;N:0", 43, null, null, null, 6620599, 5230020, 5371347, 7164065, 0, "SRX21885942", "SRS18977067", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.55183, null, 0.13531, null, 0.99105, null, 0.54904, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26577, "SRR26173878", "SRX21885941", "SRS18977064", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 C22 R1", "GSM7804133", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 C22 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804133", "GSM7804133: V2a sample2 354 C22 R1; Danio rerio; RNA Seq", "GSM7804133 r1", "GSM7804133", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_C22_R1.fastq.gz", "fastq", 35984550.0, 836850.0, "GSM7804133 r1", "0:43", "A:9917644;C:7959027;G:8126203;T:9981676;N:0", 43, null, null, null, 9917644, 7959027, 8126203, 9981676, 0, "SRX21885941", "SRS18977064", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85473, null, 0.2804, null, 0.91165, null, 0.52909, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26578, "SRR26173879", "SRX21885940", "SRS18977065", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 C21 R1", "GSM7804132", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 C21 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804132", "GSM7804132: V2a sample2 354 C21 R1; Danio rerio; RNA Seq", "GSM7804132 r1", "GSM7804132", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_C21_R1.fastq.gz", "fastq", 32265738.0, 750366.0, "GSM7804132 r1", "0:43", "A:8963112;C:7046873;G:7192067;T:9063686;N:0", 43, null, null, null, 8963112, 7046873, 7192067, 9063686, 0, "SRX21885940", "SRS18977065", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.8426, null, 0.36876, null, 0.91179, null, 0.58759, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26579, "SRR26173880", "SRX21885939", "SRS18977066", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 C20 R1", "GSM7804131", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 C20 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804131", "GSM7804131: V2a sample2 354 C20 R1; Danio rerio; RNA Seq", "GSM7804131 r1", "GSM7804131", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_C20_R1.fastq.gz", "fastq", 33471157.0, 778399.0, "GSM7804131 r1", "0:43", "A:9073629;C:7510863;G:7675381;T:9211284;N:0", 43, null, null, null, 9073629, 7510863, 7675381, 9211284, 0, "SRX21885939", "SRS18977066", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.82141, null, 0.28926, null, 0.93655, null, 0.49873, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26580, "SRR26173881", "SRX21885938", "SRS18977062", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 C19 R1", "GSM7804130", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 C19 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804130", "GSM7804130: V2a sample2 354 C19 R1; Danio rerio; RNA Seq", "GSM7804130 r1", "GSM7804130", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_C19_R1.fastq.gz", "fastq", 30131304.0, 700728.0, "GSM7804130 r1", "0:43", "A:8036932;C:6893678;G:7034855;T:8165839;N:0", 43, null, null, null, 8036932, 6893678, 7034855, 8165839, 0, "SRX21885938", "SRS18977062", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.80896, null, 0.25245, null, 0.94067, null, 0.54072, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26581, "SRR26173882", "SRX21885937", "SRS18977061", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 C18 R1", "GSM7804129", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 C18 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804129", "GSM7804129: V2a sample2 354 C18 R1; Danio rerio; RNA Seq", "GSM7804129 r1", "GSM7804129", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_C18_R1.fastq.gz", "fastq", 31050429.0, 722103.0, "GSM7804129 r1", "0:43", "A:8363024;C:7088111;G:7227301;T:8371993;N:0", 43, null, null, null, 8363024, 7088111, 7227301, 8371993, 0, "SRX21885937", "SRS18977061", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87399, null, 0.20843, null, 0.89881, null, 0.49682, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26582, "SRR26173883", "SRX21885936", "SRS18977063", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 B17 R1", "GSM7804104", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 B17 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804104", "GSM7804104: V2a sample2 354 B17 R1; Danio rerio; RNA Seq", "GSM7804104 r1", "GSM7804104", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_B17_R1.fastq.gz", "fastq", 47093729.0, 1095203.0, "GSM7804104 r1", "0:43", "A:13057598;C:10185883;G:10457076;T:13393172;N:0", 43, null, null, null, 13057598, 10185883, 10457076, 13393172, 0, "SRX21885936", "SRS18977063", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.80343, null, 0.36098, null, 0.95059, null, 0.52562, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26583, "SRR26173884", "SRX21885935", "SRS18977060", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 B16 R1", "GSM7804103", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 B16 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804103", "GSM7804103: V2a sample2 354 B16 R1; Danio rerio; RNA Seq", "GSM7804103 r1", "GSM7804103", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_B16_R1.fastq.gz", "fastq", 34160791.0, 794437.0, "GSM7804103 r1", "0:43", "A:9178469;C:7729053;G:7901331;T:9351938;N:0", 43, null, null, null, 9178469, 7729053, 7901331, 9351938, 0, "SRX21885935", "SRS18977060", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.79028, null, 0.25695, null, 0.94627, null, 0.51668, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26584, "SRR26173885", "SRX21885934", "SRS18977059", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 B15 R1", "GSM7804102", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 B15 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804102", "GSM7804102: V2a sample2 354 B15 R1; Danio rerio; RNA Seq", "GSM7804102 r1", "GSM7804102", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_B15_R1.fastq.gz", "fastq", 29152495.0, 677965.0, "GSM7804102 r1", "0:43", "A:7966546;C:6516464;G:6675123;T:7994362;N:0", 43, null, null, null, 7966546, 6516464, 6675123, 7994362, 0, "SRX21885934", "SRS18977059", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.83832, null, 0.25969, null, 0.92673, null, 0.51661, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26585, "SRR26173886", "SRX21885933", "SRS18977057", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 B14 R1", "GSM7804101", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 B14 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804101", "GSM7804101: V2a sample2 354 B14 R1; Danio rerio; RNA Seq", "GSM7804101 r1", "GSM7804101", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_B14_R1.fastq.gz", "fastq", 23811379.0, 553753.0, "GSM7804101 r1", "0:43", "A:6532691;C:5215122;G:5353003;T:6710563;N:0", 43, null, null, null, 6532691, 5215122, 5353003, 6710563, 0, "SRX21885933", "SRS18977057", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.74067, null, 0.3282, null, 0.95272, null, 0.49582, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26586, "SRR26173887", "SRX21885932", "SRS18977058", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 B13 R1", "GSM7804100", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 B13 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804100", "GSM7804100: V2a sample2 354 B13 R1; Danio rerio; RNA Seq", "GSM7804100 r1", "GSM7804100", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_B13_R1.fastq.gz", "fastq", 18141356.0, 421892.0, "GSM7804100 r1", "0:43", "A:4926550;C:4092334;G:4186281;T:4936191;N:0", 43, null, null, null, 4926550, 4092334, 4186281, 4936191, 0, "SRX21885932", "SRS18977058", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87463, null, 0.22642, null, 0.89826, null, 0.50541, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26587, "SRR26173888", "SRX21885931", "SRS18977056", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 B12 R1", "GSM7804099", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 B12 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804099", "GSM7804099: V2a sample2 354 B12 R1; Danio rerio; RNA Seq", "GSM7804099 r1", "GSM7804099", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_B12_R1.fastq.gz", "fastq", 34932039.0, 812373.0, "GSM7804099 r1", "0:43", "A:9555191;C:7704451;G:7897587;T:9774810;N:0", 43, null, null, null, 9555191, 7704451, 7897587, 9774810, 0, "SRX21885931", "SRS18977056", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.80402, null, 0.30224, null, 0.93592, null, 0.53659, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26588, "SRR26173889", "SRX21885930", "SRS18977055", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 B11 R1", "GSM7804098", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 B11 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804098", "GSM7804098: V2a sample2 354 B11 R1; Danio rerio; RNA Seq", "GSM7804098 r1", "GSM7804098", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_B11_R1.fastq.gz", "fastq", 35987087.0, 836909.0, "GSM7804098 r1", "0:43", "A:9801738;C:8047161;G:8248020;T:9890168;N:0", 43, null, null, null, 9801738, 8047161, 8248020, 9890168, 0, "SRX21885930", "SRS18977055", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.81805, null, 0.24526, null, 0.92092, null, 0.54523, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26589, "SRR26173890", "SRX21885929", "SRS18977054", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 B10 R1", "GSM7804097", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 B10 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804097", "GSM7804097: V2a sample2 354 B10 R1; Danio rerio; RNA Seq", "GSM7804097 r1", "GSM7804097", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_B10_R1.fastq.gz", "fastq", 33252846.0, 773322.0, "GSM7804097 r1", "0:43", "A:8996915;C:7433025;G:7633859;T:9189047;N:0", 43, null, null, null, 8996915, 7433025, 7633859, 9189047, 0, "SRX21885929", "SRS18977054", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.78892, null, 0.28622, null, 0.94237, null, 0.53023, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26590, "SRR26173891", "SRX21885928", "SRS18977053", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 A9 R1", "GSM7804072", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 A9 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804072", "GSM7804072: V2a sample2 354 A9 R1; Danio rerio; RNA Seq", "GSM7804072 r1", "GSM7804072", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_A9_R1.fastq.gz", "fastq", 23658600.0, 550200.0, "GSM7804072 r1", "0:43", "A:6447300;C:5342358;G:5472128;T:6396814;N:0", 43, null, null, null, 6447300, 5342358, 5472128, 6396814, 0, "SRX21885928", "SRS18977053", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86727, null, 0.23136, null, 0.8996, null, 0.52692, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26591, "SRR26173892", "SRX21885927", "SRS18977051", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 A8 R1", "GSM7804071", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 A8 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804071", "GSM7804071: V2a sample2 354 A8 R1; Danio rerio; RNA Seq", "GSM7804071 r1", "GSM7804071", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_A8_R1.fastq.gz", "fastq", 18645187.0, 433609.0, "GSM7804071 r1", "0:43", "A:5151340;C:4145072;G:4243308;T:5105467;N:0", 43, null, null, null, 5151340, 4145072, 4243308, 5105467, 0, "SRX21885927", "SRS18977051", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86561, null, 0.28633, null, 0.89438, null, 0.53463, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26592, "SRR26173893", "SRX21885926", "SRS18977052", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 A7 R1", "GSM7804070", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 A7 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804070", "GSM7804070: V2a sample2 354 A7 R1; Danio rerio; RNA Seq", "GSM7804070 r1", "GSM7804070", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_A7_R1.fastq.gz", "fastq", 42340466.0, 984662.0, "GSM7804070 r1", "0:43", "A:11373539;C:9660020;G:9840242;T:11466665;N:0", 43, null, null, null, 11373539, 9660020, 9840242, 11466665, 0, "SRX21885926", "SRS18977052", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.81646, null, 0.24599, null, 0.93833, null, 0.57817, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26593, "SRR26173894", "SRX21885925", "SRS18977050", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 A6 R1", "GSM7804069", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 A6 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804069", "GSM7804069: V2a sample2 354 A6 R1; Danio rerio; RNA Seq", "GSM7804069 r1", "GSM7804069", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_A6_R1.fastq.gz", "fastq", 23486858.0, 546206.0, "GSM7804069 r1", "0:43", "A:6654369;C:4998242;G:5115579;T:6718668;N:0", 43, null, null, null, 6654369, 4998242, 5115579, 6718668, 0, "SRX21885925", "SRS18977050", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.84122, null, 0.57245, null, 0.77794, null, 0.53266, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26594, "SRR26173895", "SRX21885924", "SRS18977048", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 A5 R1", "GSM7804068", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 A5 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804068", "GSM7804068: V2a sample2 354 A5 R1; Danio rerio; RNA Seq", "GSM7804068 r1", "GSM7804068", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_A5_R1.fastq.gz", "fastq", 46876450.0, 1090150.0, "GSM7804068 r1", "0:43", "A:12599291;C:10693086;G:10940020;T:12644053;N:0", 43, null, null, null, 12599291, 10693086, 10940020, 12644053, 0, "SRX21885924", "SRS18977048", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86707, null, 0.22085, null, 0.89412, null, 0.51257, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26595, "SRR26173896", "SRX21885923", "SRS18977049", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 A4 R1", "GSM7804067", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 A4 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804067", "GSM7804067: V2a sample2 354 A4 R1; Danio rerio; RNA Seq", "GSM7804067 r1", "GSM7804067", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_A4_R1.fastq.gz", "fastq", 43487233.0, 1011331.0, "GSM7804067 r1", "0:43", "A:11900913;C:9677048;G:9921622;T:11987650;N:0", 43, null, null, null, 11900913, 9677048, 9921622, 11987650, 0, "SRX21885923", "SRS18977049", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.8409, null, 0.27122, null, 0.91165, null, 0.55221, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26596, "SRR26173897", "SRX21885922", "SRS18977047", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 A3 R1", "GSM7804066", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 A3 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804066", "GSM7804066: V2a sample2 354 A3 R1; Danio rerio; RNA Seq", "GSM7804066 r1", "GSM7804066", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_A3_R1.fastq.gz", "fastq", 44287248.0, 1029936.0, "GSM7804066 r1", "0:43", "A:12065729;C:9907516;G:10143806;T:12170197;N:0", 43, null, null, null, 12065729, 9907516, 10143806, 12170197, 0, "SRX21885922", "SRS18977047", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.80982, null, 0.29232, null, 0.93675, null, 0.5661, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26597, "SRR26173898", "SRX21885921", "SRS18977046", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 A2 R1", "GSM7804065", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 A2 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804065", "GSM7804065: V2a sample2 354 A2 R1; Danio rerio; RNA Seq", "GSM7804065 r1", "GSM7804065", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_A2_R1.fastq.gz", "fastq", 39822515.0, 926105.0, "GSM7804065 r1", "0:43", "A:10662390;C:9155016;G:9361757;T:10643352;N:0", 43, null, null, null, 10662390, 9155016, 9361757, 10643352, 0, "SRX21885921", "SRS18977046", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.88377, null, 0.19244, null, 0.88627, null, 0.52412, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26598, "SRR26173899", "SRX21885920", "SRS18977044", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 P1 R1", "GSM7804040", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 P1 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804040", "GSM7804040: V2a sample1 353 P1 R1; Danio rerio; RNA Seq", "GSM7804040 r1", "GSM7804040", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_P1_R1.fastq.gz", "fastq", 35622877.0, 828439.0, "GSM7804040 r1", "0:43", "A:10094838;C:7580955;G:7760837;T:10186247;N:0", 43, null, null, null, 10094838, 7580955, 7760837, 10186247, 0, "SRX21885920", "SRS18977044", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.82753, null, 0.38743, null, 0.94085, null, 0.70753, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26599, "SRR26173900", "SRX21885919", "SRS18977045", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 O24 R1", "GSM7804039", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 O24 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804039", "GSM7804039: V2a sample1 353 O24 R1; Danio rerio; RNA Seq", "GSM7804039 r1", "GSM7804039", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_O24_R1.fastq.gz", "fastq", 25162482.0, 585174.0, "GSM7804039 r1", "0:43", "A:6589034;C:5708817;G:5862315;T:7002316;N:0", 43, null, null, null, 6589034, 5708817, 5862315, 7002316, 0, "SRX21885919", "SRS18977045", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.50646, null, 0.15797, null, 0.99086, null, 0.48626, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26600, "SRR26173901", "SRX21885918", "SRS18977043", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 O23 R1", "GSM7804038", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 O23 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804038", "GSM7804038: V2a sample1 353 O23 R1; Danio rerio; RNA Seq", "GSM7804038 r1", "GSM7804038", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_O23_R1.fastq.gz", "fastq", 21378396.0, 497172.0, "GSM7804038 r1", "0:43", "A:5419690;C:4870276;G:5019946;T:6068484;N:0", 43, null, null, null, 5419690, 4870276, 5019946, 6068484, 0, "SRX21885918", "SRS18977043", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.4177, null, 0.18826, null, 0.99344, null, 0.78066, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26601, "SRR26173902", "SRX21885917", "SRS18977042", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 O22 R1", "GSM7804037", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 O22 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804037", "GSM7804037: V2a sample1 353 O22 R1; Danio rerio; RNA Seq", "GSM7804037 r1", "GSM7804037", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_O22_R1.fastq.gz", "fastq", 30321665.0, 705155.0, "GSM7804037 r1", "0:43", "A:8123534;C:6839326;G:6921711;T:8437094;N:0", 43, null, null, null, 8123534, 6839326, 6921711, 8437094, 0, "SRX21885917", "SRS18977042", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.76574, null, 0.24445, null, 0.94014, null, 0.51811, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26602, "SRR26173903", "SRX21885916", "SRS18977041", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 O21 R1", "GSM7804036", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 O21 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804036", "GSM7804036: V2a sample1 353 O21 R1; Danio rerio; RNA Seq", "GSM7804036 r1", "GSM7804036", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_O21_R1.fastq.gz", "fastq", 24544916.0, 570812.0, "GSM7804036 r1", "0:43", "A:6528543;C:5656479;G:5771413;T:6588481;N:0", 43, null, null, null, 6528543, 5656479, 5771413, 6588481, 0, "SRX21885916", "SRS18977041", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87756, null, 0.17329, null, 0.88124, null, 0.51427, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26603, "SRR26173904", "SRX21885915", "SRS18977040", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 O20 R1", "GSM7804035", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 O20 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804035", "GSM7804035: V2a sample1 353 O20 R1; Danio rerio; RNA Seq", "GSM7804035 r1", "GSM7804035", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_O20_R1.fastq.gz", "fastq", 27471324.0, 638868.0, "GSM7804035 r1", "0:43", "A:7349212;C:6154048;G:6323796;T:7644268;N:0", 43, null, null, null, 7349212, 6154048, 6323796, 7644268, 0, "SRX21885915", "SRS18977040", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.7529, null, 0.26778, null, 0.94635, null, 0.5148, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26604, "SRR26173905", "SRX21885914", "SRS18977039", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 O19 R1", "GSM7804034", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 O19 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804034", "GSM7804034: V2a sample1 353 O19 R1; Danio rerio; RNA Seq", "GSM7804034 r1", "GSM7804034", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_O19_R1.fastq.gz", "fastq", 24908137.0, 579259.0, "GSM7804034 r1", "0:43", "A:6706594;C:5634956;G:5764632;T:6801955;N:0", 43, null, null, null, 6706594, 5634956, 5764632, 6801955, 0, "SRX21885914", "SRS18977039", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.8525, null, 0.23739, null, 0.90694, null, 0.5194, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26605, "SRR26173906", "SRX21885913", "SRS18977038", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 O18 R1", "GSM7804033", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 O18 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804033", "GSM7804033: V2a sample1 353 O18 R1; Danio rerio; RNA Seq", "GSM7804033 r1", "GSM7804033", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_O18_R1.fastq.gz", "fastq", 23328790.0, 542530.0, "GSM7804033 r1", "0:43", "A:6296932;C:5290824;G:5423100;T:6317934;N:0", 43, null, null, null, 6296932, 5290824, 5423100, 6317934, 0, "SRX21885913", "SRS18977038", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87485, null, 0.19256, null, 0.88422, null, 0.46891, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26606, "SRR26173907", "SRX21885912", "SRS18977037", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 N17 R1", "GSM7804008", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 N17 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804008", "GSM7804008: V2a sample1 353 N17 R1; Danio rerio; RNA Seq", "GSM7804008 r1", "GSM7804008", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_N17_R1.fastq.gz", "fastq", 20379592.0, 473944.0, "GSM7804008 r1", "0:43", "A:5592768;C:4503044;G:4602811;T:5680969;N:0", 43, null, null, null, 5592768, 4503044, 4602811, 5680969, 0, "SRX21885912", "SRS18977037", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.84619, null, 0.24373, null, 0.94095, null, 0.4423, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26607, "SRR26173908", "SRX21885911", "SRS18977035", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 N16 R1", "GSM7804007", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 N16 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804007", "GSM7804007: V2a sample1 353 N16 R1; Danio rerio; RNA Seq", "GSM7804007 r1", "GSM7804007", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_N16_R1.fastq.gz", "fastq", 14151343.0, 329101.0, "GSM7804007 r1", "0:43", "A:3796916;C:3223155;G:3290919;T:3840353;N:0", 43, null, null, null, 3796916, 3223155, 3290919, 3840353, 0, "SRX21885911", "SRS18977035", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85097, null, 0.21705, null, 0.93097, null, 0.52334, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26608, "SRR26173909", "SRX21885910", "SRS18977036", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 N15 R1", "GSM7804006", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 N15 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804006", "GSM7804006: V2a sample1 353 N15 R1; Danio rerio; RNA Seq", "GSM7804006 r1", "GSM7804006", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_N15_R1.fastq.gz", "fastq", 16536209.0, 384563.0, "GSM7804006 r1", "0:43", "A:4473687;C:3744698;G:3838620;T:4479204;N:0", 43, null, null, null, 4473687, 3744698, 3838620, 4479204, 0, "SRX21885910", "SRS18977036", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.88744, null, 0.19834, null, 0.89966, null, 0.5281, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26609, "SRR26173910", "SRX21885909", "SRS18977034", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 N14 R1", "GSM7804005", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 N14 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804005", "GSM7804005: V2a sample1 353 N14 R1; Danio rerio; RNA Seq", "GSM7804005 r1", "GSM7804005", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_N14_R1.fastq.gz", "fastq", 16039215.0, 373005.0, "GSM7804005 r1", "0:43", "A:4355837;C:3605999;G:3695364;T:4382015;N:0", 43, null, null, null, 4355837, 3605999, 3695364, 4382015, 0, "SRX21885909", "SRS18977034", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86632, null, 0.22226, null, 0.90268, null, 0.5092, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26610, "SRR26173911", "SRX21885908", "SRS18977033", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 N13 R1", "GSM7804004", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 N13 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804004", "GSM7804004: V2a sample1 353 N13 R1; Danio rerio; RNA Seq", "GSM7804004 r1", "GSM7804004", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_N13_R1.fastq.gz", "fastq", 15280910.0, 355370.0, "GSM7804004 r1", "0:43", "A:4072742;C:3469231;G:3555056;T:4183881;N:0", 43, null, null, null, 4072742, 3469231, 3555056, 4183881, 0, "SRX21885908", "SRS18977033", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.73874, null, 0.31529, null, 0.95988, null, 0.5442, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26611, "SRR26173912", "SRX21885907", "SRS18977032", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 N12 R1", "GSM7804003", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 N12 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804003", "GSM7804003: V2a sample1 353 N12 R1; Danio rerio; RNA Seq", "GSM7804003 r1", "GSM7804003", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_N12_R1.fastq.gz", "fastq", 10529926.0, 244882.0, "GSM7804003 r1", "0:43", "A:2835885;C:2354590;G:2390746;T:2948705;N:0", 43, null, null, null, 2835885, 2354590, 2390746, 2948705, 0, "SRX21885907", "SRS18977032", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.74571, null, 0.36729, null, 0.9443, null, 0.77069, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26612, "SRR26173913", "SRX21885906", "SRS18977030", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 N11 R1", "GSM7804002", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 N11 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804002", "GSM7804002: V2a sample1 353 N11 R1; Danio rerio; RNA Seq", "GSM7804002 r1", "GSM7804002", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_N11_R1.fastq.gz", "fastq", 21706271.0, 504797.0, "GSM7804002 r1", "0:43", "A:5853146;C:4922477;G:5009970;T:5920678;N:0", 43, null, null, null, 5853146, 4922477, 5009970, 5920678, 0, "SRX21885906", "SRS18977030", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.8394, null, 0.23984, null, 0.93468, null, 0.51881, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26613, "SRR26173914", "SRX21885905", "SRS18977031", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 N10 R1", "GSM7804001", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 N10 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804001", "GSM7804001: V2a sample1 353 N10 R1; Danio rerio; RNA Seq", "GSM7804001 r1", "GSM7804001", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_N10_R1.fastq.gz", "fastq", 22772585.0, 529595.0, "GSM7804001 r1", "0:43", "A:6225918;C:5071489;G:5184079;T:6291099;N:0", 43, null, null, null, 6225918, 5071489, 5184079, 6291099, 0, "SRX21885905", "SRS18977031", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.83486, null, 0.27703, null, 0.92433, null, 0.54887, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26614, "SRR26173915", "SRX21885904", "SRS18977029", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 M9 R1", "GSM7803976", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 M9 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803976", "GSM7803976: V2a sample1 353 M9 R1; Danio rerio; RNA Seq", "GSM7803976 r1", "GSM7803976", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_M9_R1.fastq.gz", "fastq", 19698730.0, 458110.0, "GSM7803976 r1", "0:43", "A:5282525;C:4494162;G:4591316;T:5330727;N:0", 43, null, null, null, 5282525, 4494162, 4591316, 5330727, 0, "SRX21885904", "SRS18977029", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.8598, null, 0.23744, null, 0.90871, null, 0.52081, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26615, "SRR26173916", "SRX21885903", "SRS18977028", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 M8 R1", "GSM7803975", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 M8 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803975", "GSM7803975: V2a sample1 353 M8 R1; Danio rerio; RNA Seq", "GSM7803975 r1", "GSM7803975", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_M8_R1.fastq.gz", "fastq", 19646485.0, 456895.0, "GSM7803975 r1", "0:43", "A:5214519;C:4539724;G:4616920;T:5275322;N:0", 43, null, null, null, 5214519, 4539724, 4616920, 5275322, 0, "SRX21885903", "SRS18977028", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.82407, null, 0.22367, null, 0.94298, null, 0.50209, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26616, "SRR26173917", "SRX21885902", "SRS18977025", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 M7 R1", "GSM7803974", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 M7 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803974", "GSM7803974: V2a sample1 353 M7 R1; Danio rerio; RNA Seq", "GSM7803974 r1", "GSM7803974", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_M7_R1.fastq.gz", "fastq", 7333994.0, 170558.0, "GSM7803974 r1", "0:43", "A:1958042;C:1671444;G:1690497;T:2014011;N:0", 43, null, null, null, 1958042, 1671444, 1690497, 2014011, 0, "SRX21885902", "SRS18977025", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.77392, null, 0.29548, null, 0.95114, null, 0.51367, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26617, "SRR26173918", "SRX21885901", "SRS18977027", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 M6 R1", "GSM7803973", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 M6 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803973", "GSM7803973: V2a sample1 353 M6 R1; Danio rerio; RNA Seq", "GSM7803973 r1", "GSM7803973", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_M6_R1.fastq.gz", "fastq", 23546413.0, 547591.0, "GSM7803973 r1", "0:43", "A:6369803;C:5317401;G:5430197;T:6429012;N:0", 43, null, null, null, 6369803, 5317401, 5430197, 6429012, 0, "SRX21885901", "SRS18977027", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85602, null, 0.25223, null, 0.92654, null, 0.5306, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26618, "SRR26173919", "SRX21885900", "SRS18977026", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 M5 R1", "GSM7803972", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 M5 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803972", "GSM7803972: V2a sample1 353 M5 R1; Danio rerio; RNA Seq", "GSM7803972 r1", "GSM7803972", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_M5_R1.fastq.gz", "fastq", 32919424.0, 765568.0, "GSM7803972 r1", "0:43", "A:8685316;C:7623131;G:7771679;T:8839298;N:0", 43, null, null, null, 8685316, 7623131, 7771679, 8839298, 0, "SRX21885900", "SRS18977026", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.80691, null, 0.23128, null, 0.95404, null, 0.45556, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26619, "SRR26173920", "SRX21885899", "SRS18977024", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 M4 R1", "GSM7803971", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 M4 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803971", "GSM7803971: V2a sample1 353 M4 R1; Danio rerio; RNA Seq", "GSM7803971 r1", "GSM7803971", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_M4_R1.fastq.gz", "fastq", 27743858.0, 645206.0, "GSM7803971 r1", "0:43", "A:7502879;C:6275733;G:6399007;T:7566239;N:0", 43, null, null, null, 7502879, 6275733, 6399007, 7566239, 0, "SRX21885899", "SRS18977024", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.84534, null, 0.24169, null, 0.92131, null, 0.52033, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26620, "SRR26173921", "SRX21885898", "SRS18977023", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 M3 R1", "GSM7803970", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 M3 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803970", "GSM7803970: V2a sample1 353 M3 R1; Danio rerio; RNA Seq", "GSM7803970 r1", "GSM7803970", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_M3_R1.fastq.gz", "fastq", 31646753.0, 735971.0, "GSM7803970 r1", "0:43", "A:8540660;C:7169606;G:7344972;T:8591515;N:0", 43, null, null, null, 8540660, 7169606, 7344972, 8591515, 0, "SRX21885898", "SRS18977023", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86607, null, 0.22984, null, 0.90905, null, 0.52816, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26621, "SRR26173922", "SRX21885897", "SRS18977019", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 M2 R1", "GSM7803969", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 M2 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803969", "GSM7803969: V2a sample1 353 M2 R1; Danio rerio; RNA Seq", "GSM7803969 r1", "GSM7803969", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_M2_R1.fastq.gz", "fastq", 18262487.0, 424709.0, "GSM7803969 r1", "0:43", "A:4905794;C:4167223;G:4257561;T:4931909;N:0", 43, null, null, null, 4905794, 4167223, 4257561, 4931909, 0, "SRX21885897", "SRS18977019", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87727, null, 0.19789, null, 0.88327, null, 0.51404, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26622, "SRR26173923", "SRX21885896", "SRS18977022", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 L1 R1", "GSM7803944", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 L1 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803944", "GSM7803944: V2a sample1 353 L1 R1; Danio rerio; RNA Seq", "GSM7803944 r1", "GSM7803944", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_L1_R1.fastq.gz", "fastq", 39261064.0, 913048.0, "GSM7803944 r1", "0:43", "A:10675714;C:8831605;G:9068828;T:10684917;N:0", 43, null, null, null, 10675714, 8831605, 9068828, 10684917, 0, "SRX21885896", "SRS18977022", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87519, null, 0.20246, null, 0.89696, null, 0.53416, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26623, "SRR26173924", "SRX21885895", "SRS18977020", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 K24 R1", "GSM7803943", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 K24 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803943", "GSM7803943: V2a sample1 353 K24 R1; Danio rerio; RNA Seq", "GSM7803943 r1", "GSM7803943", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_K24_R1.fastq.gz", "fastq", 10877753.0, 252971.0, "GSM7803943 r1", "0:43", "A:2828581;C:2427642;G:2504205;T:3117325;N:0", 43, null, null, null, 2828581, 2427642, 2504205, 3117325, 0, "SRX21885895", "SRS18977020", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.43358, null, 0.14805, null, 0.96483, null, 0.89489, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26624, "SRR26173925", "SRX21885894", "SRS18977021", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 K23 R1", "GSM7803942", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 K23 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803942", "GSM7803942: V2a sample1 353 K23 R1; Danio rerio; RNA Seq", "GSM7803942 r1", "GSM7803942", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_K23_R1.fastq.gz", "fastq", 11967287.0, 278309.0, "GSM7803942 r1", "0:43", "A:3236216;C:2487815;G:2583125;T:3660131;N:0", 43, null, null, null, 3236216, 2487815, 2583125, 3660131, 0, "SRX21885894", "SRS18977021", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.45352, null, 0.10712, null, 0.99249, null, 0.66514, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26625, "SRR26173926", "SRX21885893", "SRS18977016", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 K22 R1", "GSM7803941", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 K22 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803941", "GSM7803941: V2a sample1 353 K22 R1; Danio rerio; RNA Seq", "GSM7803941 r1", "GSM7803941", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_K22_R1.fastq.gz", "fastq", 27851702.0, 647714.0, "GSM7803941 r1", "0:43", "A:7549377;C:6154745;G:6313649;T:7833931;N:0", 43, null, null, null, 7549377, 6154745, 6313649, 7833931, 0, "SRX21885893", "SRS18977016", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.75496, null, 0.26752, null, 0.9472, null, 0.55385, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26626, "SRR26173927", "SRX21885892", "SRS18977017", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 K21 R1", "GSM7803940", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 K21 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803940", "GSM7803940: V2a sample1 353 K21 R1; Danio rerio; RNA Seq", "GSM7803940 r1", "GSM7803940", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_K21_R1.fastq.gz", "fastq", 25669151.0, 596957.0, "GSM7803940 r1", "0:43", "A:6873604;C:5886019;G:6019889;T:6889639;N:0", 43, null, null, null, 6873604, 5886019, 6019889, 6889639, 0, "SRX21885892", "SRS18977017", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.88089, null, 0.15861, null, 0.87988, null, 0.53381, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26627, "SRR26173928", "SRX21885891", "SRS18977018", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 K20 R1", "GSM7803939", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 K20 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803939", "GSM7803939: V2a sample1 353 K20 R1; Danio rerio; RNA Seq", "GSM7803939 r1", "GSM7803939", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_K20_R1.fastq.gz", "fastq", 21481940.0, 499580.0, "GSM7803939 r1", "0:43", "A:5797700;C:4860618;G:4983240;T:5840382;N:0", 43, null, null, null, 5797700, 4860618, 4983240, 5840382, 0, "SRX21885891", "SRS18977018", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86105, null, 0.23237, null, 0.90134, null, 0.52076, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26628, "SRR26173929", "SRX21885890", "SRS18977014", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 K19 R1", "GSM7803938", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 K19 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803938", "GSM7803938: V2a sample1 353 K19 R1; Danio rerio; RNA Seq", "GSM7803938 r1", "GSM7803938", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_K19_R1.fastq.gz", "fastq", 23007709.0, 535063.0, "GSM7803938 r1", "0:43", "A:6158988;C:5204570;G:5321940;T:6322211;N:0", 43, null, null, null, 6158988, 5204570, 5321940, 6322211, 0, "SRX21885890", "SRS18977014", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.78733, null, 0.25377, null, 0.94556, null, 0.53829, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26629, "SRR26173930", "SRX21885889", "SRS18977015", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 K18 R1", "GSM7803937", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 K18 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803937", "GSM7803937: V2a sample1 353 K18 R1; Danio rerio; RNA Seq", "GSM7803937 r1", "GSM7803937", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_K18_R1.fastq.gz", "fastq", 25088565.0, 583455.0, "GSM7803937 r1", "0:43", "A:6762035;C:5659600;G:5805722;T:6861208;N:0", 43, null, null, null, 6762035, 5659600, 5805722, 6861208, 0, "SRX21885889", "SRS18977015", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.83379, null, 0.22893, null, 0.9251, null, 0.51495, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26630, "SRR26173931", "SRX21885888", "SRS18977011", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 J17 R1", "GSM7803912", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 J17 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803912", "GSM7803912: V2a sample1 353 J17 R1; Danio rerio; RNA Seq", "GSM7803912 r1", "GSM7803912", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_J17_R1.fastq.gz", "fastq", 24235359.0, 563613.0, "GSM7803912 r1", "0:43", "A:6687906;C:5244266;G:5377965;T:6925222;N:0", 43, null, null, null, 6687906, 5244266, 5377965, 6925222, 0, "SRX21885888", "SRS18977011", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.80212, null, 0.29984, null, 0.94769, null, 0.57954, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26631, "SRR26173932", "SRX21885887", "SRS18977013", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 J16 R1", "GSM7803911", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 J16 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803911", "GSM7803911: V2a sample1 353 J16 R1; Danio rerio; RNA Seq", "GSM7803911 r1", "GSM7803911", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_J16_R1.fastq.gz", "fastq", 27111973.0, 630511.0, "GSM7803911 r1", "0:43", "A:7217001;C:6181115;G:6340909;T:7372948;N:0", 43, null, null, null, 7217001, 6181115, 6340909, 7372948, 0, "SRX21885887", "SRS18977013", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.71684, null, 0.26529, null, 0.94491, null, 0.50602, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26632, "SRR26173933", "SRX21885886", "SRS18977010", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 J15 R1", "GSM7803910", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 J15 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803910", "GSM7803910: V2a sample1 353 J15 R1; Danio rerio; RNA Seq", "GSM7803910 r1", "GSM7803910", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_J15_R1.fastq.gz", "fastq", 23290391.0, 541637.0, "GSM7803910 r1", "0:43", "A:6290890;C:5279983;G:5398604;T:6320914;N:0", 43, null, null, null, 6290890, 5279983, 5398604, 6320914, 0, "SRX21885886", "SRS18977010", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85285, null, 0.2328, null, 0.92214, null, 0.51744, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26633, "SRR26173934", "SRX21885885", "SRS18977012", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 J14 R1", "GSM7803909", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 J14 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803909", "GSM7803909: V2a sample1 353 J14 R1; Danio rerio; RNA Seq", "GSM7803909 r1", "GSM7803909", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_J14_R1.fastq.gz", "fastq", 22177637.0, 515759.0, "GSM7803909 r1", "0:43", "A:5946858;C:4992625;G:5124052;T:6114102;N:0", 43, null, null, null, 5946858, 4992625, 5124052, 6114102, 0, "SRX21885885", "SRS18977012", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.75767, null, 0.28218, null, 0.95394, null, 0.44926, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26634, "SRR26173935", "SRX21885884", "SRS18977009", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 J13 R1", "GSM7803908", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 J13 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803908", "GSM7803908: V2a sample1 353 J13 R1; Danio rerio; RNA Seq", "GSM7803908 r1", "GSM7803908", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_J13_R1.fastq.gz", "fastq", 25862479.0, 601453.0, "GSM7803908 r1", "0:43", "A:6973520;C:5810960;G:5943676;T:7134323;N:0", 43, null, null, null, 6973520, 5810960, 5943676, 7134323, 0, "SRX21885884", "SRS18977009", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.81395, null, 0.28506, null, 0.92801, null, 0.50957, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26635, "SRR26173936", "SRX21885883", "SRS18977008", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 J12 R1", "GSM7803907", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 J12 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803907", "GSM7803907: V2a sample1 353 J12 R1; Danio rerio; RNA Seq", "GSM7803907 r1", "GSM7803907", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_J12_R1.fastq.gz", "fastq", 21381621.0, 497247.0, "GSM7803907 r1", "0:43", "A:5870837;C:4668159;G:4791244;T:6051381;N:0", 43, null, null, null, 5870837, 4668159, 4791244, 6051381, 0, "SRX21885883", "SRS18977008", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.7505, null, 0.43605, null, 0.95639, null, 0.84845, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26636, "SRR26173937", "SRX21885882", "SRS18977006", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 J11 R1", "GSM7803906", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 J11 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803906", "GSM7803906: V2a sample1 353 J11 R1; Danio rerio; RNA Seq", "GSM7803906 r1", "GSM7803906", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_J11_R1.fastq.gz", "fastq", 23749287.0, 552309.0, "GSM7803906 r1", "0:43", "A:6394024;C:5405641;G:5544581;T:6405041;N:0", 43, null, null, null, 6394024, 5405641, 5544581, 6405041, 0, "SRX21885882", "SRS18977006", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.88044, null, 0.20802, null, 0.89327, null, 0.49819, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26637, "SRR26173938", "SRX21885881", "SRS18977005", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 J10 R1", "GSM7803905", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 J10 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803905", "GSM7803905: V2a sample1 353 J10 R1; Danio rerio; RNA Seq", "GSM7803905 r1", "GSM7803905", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_J10_R1.fastq.gz", "fastq", 29176145.0, 678515.0, "GSM7803905 r1", "0:43", "A:7791607;C:6552866;G:6732705;T:8098967;N:0", 43, null, null, null, 7791607, 6552866, 6732705, 8098967, 0, "SRX21885881", "SRS18977005", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.71479, null, 0.31461, null, 0.95937, null, 0.54763, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26638, "SRR26173939", "SRX21885880", "SRS18977007", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 I9 R1", "GSM7803880", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 I9 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803880", "GSM7803880: V2a sample1 353 I9 R1; Danio rerio; RNA Seq", "GSM7803880 r1", "GSM7803880", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_I9_R1.fastq.gz", "fastq", 24090707.0, 560249.0, "GSM7803880 r1", "0:43", "A:6543882;C:5415516;G:5557789;T:6573520;N:0", 43, null, null, null, 6543882, 5415516, 5557789, 6573520, 0, "SRX21885880", "SRS18977007", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85372, null, 0.22772, null, 0.90094, null, 0.53266, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26639, "SRR26173940", "SRX21885879", "SRS18977004", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 I8 R1", "GSM7803879", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 I8 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803879", "GSM7803879: V2a sample1 353 I8 R1; Danio rerio; RNA Seq", "GSM7803879 r1", "GSM7803879", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_I8_R1.fastq.gz", "fastq", 20394255.0, 474285.0, "GSM7803879 r1", "0:43", "A:5480008;C:4590753;G:4698367;T:5625127;N:0", 43, null, null, null, 5480008, 4590753, 4698367, 5625127, 0, "SRX21885879", "SRS18977004", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.74576, null, 0.3214, null, 0.95806, null, 0.50252, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26640, "SRR26173941", "SRX21885878", "SRS18977003", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 I7 R1", "GSM7803878", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 I7 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803878", "GSM7803878: V2a sample1 353 I7 R1; Danio rerio; RNA Seq", "GSM7803878 r1", "GSM7803878", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_I7_R1.fastq.gz", "fastq", 20725011.0, 481977.0, "GSM7803878 r1", "0:43", "A:5625880;C:4647001;G:4774993;T:5677137;N:0", 43, null, null, null, 5625880, 4647001, 4774993, 5677137, 0, "SRX21885878", "SRS18977003", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85618, null, 0.25757, null, 0.90479, null, 0.5166, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26641, "SRR26173942", "SRX21885877", "SRS18977002", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 I6 R1", "GSM7803877", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 I6 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803877", "GSM7803877: V2a sample1 353 I6 R1; Danio rerio; RNA Seq", "GSM7803877 r1", "GSM7803877", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_I6_R1.fastq.gz", "fastq", 30081467.0, 699569.0, "GSM7803877 r1", "0:43", "A:8235100;C:6659013;G:6834239;T:8353115;N:0", 43, null, null, null, 8235100, 6659013, 6834239, 8353115, 0, "SRX21885877", "SRS18977002", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.82589, null, 0.32845, null, 0.92417, null, 0.52161, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26642, "SRR26173943", "SRX21885876", "SRS18977001", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 I5 R1", "GSM7803876", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 I5 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803876", "GSM7803876: V2a sample1 353 I5 R1; Danio rerio; RNA Seq", "GSM7803876 r1", "GSM7803876", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_I5_R1.fastq.gz", "fastq", 34927911.0, 812277.0, "GSM7803876 r1", "0:43", "A:9434960;C:7894430;G:8106720;T:9491801;N:0", 43, null, null, null, 9434960, 7894430, 8106720, 9491801, 0, "SRX21885876", "SRS18977001", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86691, null, 0.23833, null, 0.90429, null, 0.52495, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26643, "SRR26173944", "SRX21885875", "SRS18977000", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 I4 R1", "GSM7803875", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 I4 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803875", "GSM7803875: V2a sample1 353 I4 R1; Danio rerio; RNA Seq", "GSM7803875 r1", "GSM7803875", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_I4_R1.fastq.gz", "fastq", 41615099.0, 967793.0, "GSM7803875 r1", "0:43", "A:11232545;C:9389292;G:9644531;T:11348731;N:0", 43, null, null, null, 11232545, 9389292, 9644531, 11348731, 0, "SRX21885875", "SRS18977000", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.84939, null, 0.24066, null, 0.90337, null, 0.50767, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26644, "SRR26173945", "SRX21885874", "SRS18976999", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample1 353 I3 R1", "GSM7803874", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample1 353 I3 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7803874", "GSM7803874: V2a sample1 353 I3 R1; Danio rerio; RNA Seq", "GSM7803874 r1", "GSM7803874", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_353_I3_R1.fastq.gz", "fastq", 34316150.0, 798050.0, "GSM7803874 r1", "0:43", "A:9271155;C:7644902;G:7871948;T:9528145;N:0", 43, null, null, null, 9271155, 7644902, 7871948, 9528145, 0, "SRX21885874", "SRS18976999", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.76458, null, 0.30549, null, 0.95649, null, 0.53971, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26645, "SRR26173772", "SRX21885873", "SRS18976998", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 L20 R1", "GSM7804347", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 L20 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804347", "GSM7804347: V2a sample2 354 L20 R1; Danio rerio; RNA Seq", "GSM7804347 r1", "GSM7804347", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_L20_R1.fastq.gz", "fastq", 29370161.0, 683027.0, "GSM7804347 r1", "0:43", "A:8415585;C:6114838;G:6265996;T:8573742;N:0", 43, null, null, null, 8415585, 6114838, 6265996, 8573742, 0, "SRX21885873", "SRS18976998", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85077, null, 0.37188, null, 0.96952, null, 0.55266, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26646, "SRR26173773", "SRX21885872", "SRS18976996", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 L19 R1", "GSM7804346", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 L19 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804346", "GSM7804346: V2a sample2 354 L19 R1; Danio rerio; RNA Seq", "GSM7804346 r1", "GSM7804346", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_L19_R1.fastq.gz", "fastq", 31064189.0, 722423.0, "GSM7804346 r1", "0:43", "A:8761668;C:6650054;G:6796322;T:8856145;N:0", 43, null, null, null, 8761668, 6650054, 6796322, 8856145, 0, "SRX21885872", "SRS18976996", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.84784, null, 0.4328, null, 0.91865, null, 0.54701, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26647, "SRR26173774", "SRX21885871", "SRS18976997", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 L18 R1", "GSM7804345", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 L18 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804345", "GSM7804345: V2a sample2 354 L18 R1; Danio rerio; RNA Seq", "GSM7804345 r1", "GSM7804345", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_L18_R1.fastq.gz", "fastq", 30281460.0, 704220.0, "GSM7804345 r1", "0:43", "A:8479926;C:6562726;G:6732082;T:8506726;N:0", 43, null, null, null, 8479926, 6562726, 6732082, 8506726, 0, "SRX21885871", "SRS18976997", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.86278, null, 0.35585, null, 0.9133, null, 0.52905, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26648, "SRR26173775", "SRX21885870", "SRS18976994", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 K17 R1", "GSM7804320", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 K17 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804320", "GSM7804320: V2a sample2 354 K17 R1; Danio rerio; RNA Seq", "GSM7804320 r1", "GSM7804320", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_K17_R1.fastq.gz", "fastq", 33586999.0, 781093.0, "GSM7804320 r1", "0:43", "A:9198057;C:7484755;G:7655890;T:9248297;N:0", 43, null, null, null, 9198057, 7484755, 7655890, 9248297, 0, "SRX21885870", "SRS18976994", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85328, null, 0.25956, null, 0.91013, null, 0.52033, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26649, "SRR26173776", "SRX21885869", "SRS18976995", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 K16 R1", "GSM7804319", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 K16 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804319", "GSM7804319: V2a sample2 354 K16 R1; Danio rerio; RNA Seq", "GSM7804319 r1", "GSM7804319", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_K16_R1.fastq.gz", "fastq", 34942961.0, 812627.0, "GSM7804319 r1", "0:43", "A:9884091;C:7477031;G:7622507;T:9959332;N:0", 43, null, null, null, 9884091, 7477031, 7622507, 9959332, 0, "SRX21885869", "SRS18976995", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.87105, null, 0.25941, null, 0.9344, null, 0.48083, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26650, "SRR26173777", "SRX21885868", "SRS18976993", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 K15 R1", "GSM7804318", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 K15 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804318", "GSM7804318: V2a sample2 354 K15 R1; Danio rerio; RNA Seq", "GSM7804318 r1", "GSM7804318", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_K15_R1.fastq.gz", "fastq", 32995577.0, 767339.0, "GSM7804318 r1", "0:43", "A:8890551;C:7526324;G:7638992;T:8939710;N:0", 43, null, null, null, 8890551, 7526324, 7638992, 8939710, 0, "SRX21885868", "SRS18976993", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.73421, null, 0.24037, null, 0.92281, null, 0.5232, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26651, "SRR26173778", "SRX21885867", "SRS18976991", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 K14 R1", "GSM7804317", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 K14 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804317", "GSM7804317: V2a sample2 354 K14 R1; Danio rerio; RNA Seq", "GSM7804317 r1", "GSM7804317", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_K14_R1.fastq.gz", "fastq", 34918709.0, 812063.0, "GSM7804317 r1", "0:43", "A:9702093;C:7610097;G:7779557;T:9826962;N:0", 43, null, null, null, 9702093, 7610097, 7779557, 9826962, 0, "SRX21885867", "SRS18976991", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.84054, null, 0.28341, null, 0.95844, null, 0.52971, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26652, "SRR26173779", "SRX21885866", "SRS18976992", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 K13 R1", "GSM7804316", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 K13 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804316", "GSM7804316: V2a sample2 354 K13 R1; Danio rerio; RNA Seq", "GSM7804316 r1", "GSM7804316", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_K13_R1.fastq.gz", "fastq", 34277278.0, 797146.0, "GSM7804316 r1", "0:43", "A:9378683;C:7633762;G:7740014;T:9524819;N:0", 43, null, null, null, 9378683, 7633762, 7740014, 9524819, 0, "SRX21885866", "SRS18976992", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.81082, null, 0.32096, null, 0.92908, null, 0.53117, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26653, "SRR26173780", "SRX21885865", "SRS18976990", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 K12 R1", "GSM7804315", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 K12 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804315", "GSM7804315: V2a sample2 354 K12 R1; Danio rerio; RNA Seq", "GSM7804315 r1", "GSM7804315", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_K12_R1.fastq.gz", "fastq", 28040429.0, 652103.0, "GSM7804315 r1", "0:43", "A:7699772;C:6248721;G:6390568;T:7701368;N:0", 43, null, null, null, 7699772, 6248721, 6390568, 7701368, 0, "SRX21885865", "SRS18976990", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.88142, null, 0.22865, null, 0.88051, null, 0.50605, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"], [26654, "SRR26173781", "SRX21885864", "SRS18976988", "SRP463130", "PRJNA1020854", "Molecular blueprints for spinal circuit modules controlling locomotor speed", "GSE243993", "Transcriptome Analysis", "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.", null, "pubmed:37919423", null, "V2a sample2 354 K11 R1", "GSM7804314", null, "source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing", "V2a sample2 354 K11 R1", "The reads from each sequenced cell were mapped to the zebrafish reference genome \u201cDanio rerio  Ensembl  GRCz11\u201d using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis", "Spinal cord", null, "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons", "GSM7804314", "GSM7804314: V2a sample2 354 K11 R1; Danio rerio; RNA Seq", "GSM7804314 r1", "GSM7804314", "1", "Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37\u00b0C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4\u00b0C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 \u03bcm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80\u00b0C. Smart Seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP463130", null, null, "SS2_18_354_K11_R1.fastq.gz", "fastq", 37066516.0, 862012.0, "GSM7804314 r1", "0:43", "A:10269237;C:8130071;G:8315363;T:10351845;N:0", 43, null, null, null, 10269237, 8130071, 8315363, 10351845, 0, "SRX21885864", "SRS18976988", "SRA1719948", "Neuroscience, Karolinaska Institutet", "Neuroscience, Karolinaska Institutet", 1, 0.85469, null, 0.39595, null, 0.87758, null, 0.52563, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-09-25", "Juvenile", "Juvenile", "Spinal Cord", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 1587, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation_coarse\" = :p0 and \"experiment.library_source\" = :p1 order by rowid limit 101", "params": {"p0": "Juvenile", "p1": "TRANSCRIPTOMIC SINGLE CELL"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 1587, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 1587, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "cDNA", "label": "cDNA", "count": 1587, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 1535, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 52, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 1587, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "Juvenile", "label": "Juvenile", "count": 1587, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "Juvenile", "label": "Juvenile", "count": 1587, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&devstage_curation=Juvenile", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "Nervous System", "label": "Nervous System", "count": 1556, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=Nervous+System", "selected": false}, {"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=Cardiovascular+System", "selected": false}, {"value": "All anatomical structures", "label": "All anatomical structures", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Hematopoietic System", "label": "Hematopoietic System", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=Hematopoietic+System", "selected": false}, {"value": "Renal System", "label": "Renal System", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=Renal+System", "selected": false}, {"value": "Endocrine System", "label": "Endocrine System", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=Endocrine+System", "selected": false}, {"value": "Muscular System", "label": "Muscular System", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation_coarse=Muscular+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "Spinal Cord", "label": "Spinal Cord", "count": 1535, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Spinal+Cord", "selected": false}, {"value": "Brain", "label": "Brain", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Brain", "selected": false}, {"value": "Heart", "label": "Heart", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Heart", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Kidney", "label": "Kidney", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Kidney", "selected": false}, {"value": "Spleen", "label": "Spleen", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Spleen", "selected": false}, {"value": "Muscle", "label": "Muscle", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Muscle", "selected": false}, {"value": "Pituitary Gland", "label": "Pituitary Gland", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Pituitary+Gland", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "results": [{"value": "smartseq", "label": "smartseq", "count": 1535, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=smartseq", "selected": false}, {"value": "10x", "label": "10x", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x", "selected": false}, {"value": "bulk", "label": "bulk", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=bulk", "selected": false}, {"value": "marsseq", "label": "marsseq", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=marsseq", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "26654", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Juvenile&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&_next=26654", "private": false, "allow_execute_sql": true, "query_ms": 133.82266400003573}